Note: Until the end of P87 (September 2011) science data have been processed by QC Garching with the best possible (certified) calibrations solutions. The products were ingested into the Science Archive and delivered to the PIs. This service has been terminated with the begin of October 2011.

The documentation of the GIRAFFE science recipe is kept here for its heritage value. All statements about science processing by QC refer to the status before October 2011.

DPR CATG = SCIENCE, DPR TYPE = OBJECT,OzPoz or OBJECT,SimCal

Raw science frame (Medusa mode); old CCD "Bruce"

new CCD "Carreras"

Note:

All Service Mode data in P80 (2007-10 ... 2008-03) have the CCD
glow background correctly removed (the bright top glow in the left image). Before
that period, background removal was not enabled; after that period, there is no
need since the new CCD has no such glow.

Processed science data from 2008-01-18 and later, taken with the
SimCal lamp on, have the wavelength scale differentially corrected with the SimCal
fibre information.

As of 2008-04-01, all SimCal data also have information provided
(in their product binary table) about barycentric, heliocentric and geocentric
RV corrections (in km/s) per fibre. Note that these values have not been applied.

Recipe. The pipeline recipe giscience
performs the full reduction of GIRAFFE science frames.

Scheme. The following steps are performed:

old CCD (up to 2008-03-13): de-bias with a scaled master bias (--bsremove-method=ZMASTER)new CCD (since 2008-05-26): de-bias with the fitted bias function taken
from the OVERSCAN region (pixels 2-49, fit is a 5th order polynomial) (--bsremove-method=PROFILE+CURVE
--bsremove-yorder=5)

remove background as defined by a master dark scaled by exposure
time (old CCD only)

find and extract the fibres, using the localization and width solutions
from the flat field

divide extracted science spectrum by extracted and normalized flat
field

correct science spectra for differences in the fibre transmission
(as recorded in the flat field)

wavelength-calibrate and resample science spectrum, using the dispersion
solution

if SimCal has been used, the wavelength scale is differentially
corrected (since 2008-01-18)

The GIRAFFE pipeline run by QC Garching on science data until October 2011 used certified
and closest-in-time calibration solutions, mostly taken during daytime
following the science night. As of 2008-01-18, the recipe took into account the signal
in the simultaneous calibration fibres (OBJECT,SimCal data). Data taken earlier do
not have this correction enabled.

Extraction. The fibre signal is extracted by summing up (average
extraction) the signal based on the localization solution of the flat field (PLOC
file, pro.catg = FF_LOCCENTROID). Note: the signal from the last one or two fibres
does usually not fall completely onto the chip. The pipeline suppresses these
fibres completely.

The pipeline version 2.5 and later can provide optimum extraction and
average extraction. For operational reasons, science data delivered by QC always
used the average extraction. That extraction mode is operationally more stable
but cannot suppress cosmic rays. The optimum extraction mode requires a modified
calibration product scheme.

Incomplete last fibre
(right); the extracted fibre signal is marked red. This is an extracted
view of a raw file, highly compressed in vertical direction in order
to emphasize the fibre signal curvature

Flat-fielding. The extracted spectra are
divided by the corresponding spectra of the flat field (PFEX file, pro.catg = FF_EXTSPECTRA).
The flat-field signal is normalized such that the collapsed spectrum of the object
fibre with the highest transmission is set to 1, and all other object fibres
are scaled relative to that fibre signal. SIMCAL fibres in the flat-field are excluded
from the statistics and always set to 1, while the SKY fibres get scaled like the
object fibres. The extracted spectrum has the instrument response curve removed
(at the price of now being affected by the lamp continuum which is however very smooth),
and to a large extent also the fringing. The figure below demonstrates the effect
of flattening: the 20nm scale ondulations are caused by the instrument response,
while the ripples on the 1-2 nm scale are due to fringing. Both effects have disappeared
after flattening.

Response. There is no response correction done by the pipeline,
nor is it currently foreseen. In Medusa mode, no standard stars are taken, in IFU
mode only on request of the user. In Argus mode, spectrophotometric standard
stars are measured routinely. These are presently processed like science
data. Their products are included in the data packages and can
be used to derive an approximate flux calibration, using the fibres with
the STD signal to derive the response curve, while the transmission scaling
of the other fibres is provided by the flat field data.

Transmission. The fibre-to-fibre response differences are corrected
using information from the fibre flats (the normalized factors from the above section
"Flat-fielding"). Their values are stored as column TRANSMISSION in
the fibre_setup table (extension 2 of the product files) and can be used to undo
the correction.

Sky correction. The sky signal is recorded in the dedicated SKY
fibres in the IFU and Argus modes. In Medusa mode, the user is completely
free to record the sky signal in any object fibre. Since the pipeline
recipe in general does not know exactly which fibres correctly record
the sky signal, the sky signal is extracted by the recipe just as for
any other fibre, and sky subtraction is left to the user.

Background subtraction. For data taken between October 2007
and March 2008, the recipe has subtracted the background as recorded in a master
dark frame. For data later than that, there is no need for subtraction (no glow in
the new CCD).

The master dark is constructed from at least 3 input raw darks (one hour exposure time each) and scaled properly for exposure time.

SimCal fibre correction. If the simultaneous calibration fibres have
been used, their signal is used to incrementally correct the wavelength scale. The
amount of the correction is available as column WLRES in the fibre_setup table (extension
2 of the product files) and can be used to undo the correction.

Since 2008-04-01, all SimCal science data also have information provided
(in their product binary table) about barycentric, heliocentric and geocentric
RV corrections (in km/s) per fibre. These corrections have not been applied by the pipeline.

Products. The following science products are created by the pipeline:

product category (PRO CATG)*

product index**

product code***

delivered?

format

comments

SCIENCE_REDUCED

0006

SRED

no

2D (pixel space)

debiased raw frame

SCIENCE_EXTSPECTRA

0002

SEXS

yes

2D, pixels vs fibre index

extracted spectra, one column per fibre

SCIENCE_EXTERRORS

0000

SEXE

yes

same as SEXS

corresponding extraction error

Main product: SCIENCE_RBNSPECTRA

0005

SRBS

yes

2D, wavelength bins vs. fibre index

rebinned extracted spectra, one column per fibre

Main product: SCIENCE_RBNERRORS

0004

SRBE

yes

same as SRBS

corresponding extraction error

SCIENCE_RCSPECTRA

0008

SIMG

yes

2D, spatial coordinates

reconstructed image (IFU and Argus)

SCIENCE_RCERRORS

0007

SIME

yes

same as SIMG

corresponding error (IFU and Argus)

SCIENCE_CUBE_SPECTRA

0009

SCUB

yes

3D, spatial and spectral coordinates

data cube with full spatial and spectral information (Argus
only)

SCIENCE_CUBE_ERRORS

0010

SCUE

yes

same as SCUB

corresponding error (Argus only)

* coded as HIERARCH.ESO.PRO.CATG in the fits header
** index of the PIPEFILE name, coded as PIPEFILE in the fits header
*** used in the delivered name

The error files (PRO.CATG = SCIENCE_EXTERRORS etc.) contain the calculated
standard deviation per pixel of the SCIENCE_EXTSPECTRA file (containing:
photon noise, read noise; the flat-field extraction errors is not included
here). This error is propagated to the error files of the rebinned spectrum
(SCIENCE_RBNERRORS) and, for IFU and Argus, of the recombined spectro-image,
SCIENCE_RCERRORS, and the datacube, SCIENCE_CUBE_ERRORS (Argus only).

Data format. All products come as FITS files with the product
pixels in the first extension, and a binary table in the second extension. That fibre_setup
table is described here.

Quality plots. Since April 2005 until October 2011, we delivered
in the data packages, and to the archive, a set of quality control plots.

Medusa. The first QC plot for the Medusa setups has the following
elements:

a crosscut through the raw frame (row @2048)

a closeup of box 1, displaying the central 200 pixels with the fibre
PSF and the BIAS level indicated by the red broken line

a S/N comparison: the mean S/N of the brightest fibre (see plot
#4) is plotted over the corresponding signal, the value is marked red; for comparison,
data points from other science observations in the same setup are overplotted;
they are read from the giraffe_science table in the QC1
database, keys brightest_s2n vs. brightest_flux. This plot is
intended to monitor any irregularity with the S/N of the reduced spectra: all similar
data points should form a square-root law, and the red data point should fall somewhere
onto that curve

a selection of spectra (rebinned for display):

a) the fibre with the lowest nominal magnitude (read from the ozpoz
table), assumed to represent the sky signal

b) the fibre with the brightest nominal magnitude (again read from
the ozpoz table; if none found, fibre 10 is displayed)

c) S/N for the fibre selected in b), derived by division of the
spectrum by the corresponding error in the RBN_ERRORS file (SRBE)

Both the signal and S/N are plotted under 'slope' with a compressed
horizontal scale. The strategy to find the faintest and the brightest
fibre assumes the usual magnitudes. If the user has chosen a different
convention, the guess may fail.

histograms:

a) the lower 0-200 counts in the product file ("prod."). 0 marks
the background, there should be no counts (other than noise) around that
value, otherwise there is a problem with background subtraction

b) the upper 60,000+ region in the raw file, indicative of a
saturation problem.

The lower panel displays, among other things, the delta in temperature
("deg") and time ("day"), resp., between the science exposure and the wavelength
calibration; these values should be small in order to be sure to have no thermal
or non-thermal drifts of the temperature-sensitive grating between science and calibration
exposures.

For spectra above 585 nm, sky emission lines are marked in #4a (red
vertical lines), and telluric absorption lines are marked in #4b (blue vertical
lines). The emission lines (at UVES resolution) are taken from Hanuschik
(2003). The list of telluric lines at the UVES resolution is not yet
published.

First QC plot for
Medusa data.

Three more QC plots for the Medusa modes display all extracted spectra,
along with their user-provided target name and magnitude:

Spectral plots. For
the Medusa modes all extracted spectra are displayed in 3 plots, along with the
user-provided target name and magnitude. This figure shows an example for fibres
1-45. n/a means 'not allocated'.

IFU, Argus. The Argus and IFU settings also have a set of QC
plots. The first one is very similar to the Medusa case, with the faintest object
fibre showed under #4a, the integrated signal from all fibres of subslit #6 under
4b, and the S/N for the first fibre from #6. This selection has been made
since Argus and IFU spectra are not independent of each other. The guess
of the faintest object may fail under the same conditions as described
in the Medusa case. The S/N comparison (plot #3) is not active for Argus/IFU since
there is no brightest fibre. The histogram checks in plot #5 are the same as for
Medusa.

QC
plot for Argus/IFU modes.

Instead of a preview of all fibres, for Argus and IFU the reconstructed
image (RCSPECTRA) is available as preview. It has been obtained by collapsing
the spectra into a single number per fibre and display that value on a
relative spatial grid. The mapping between fibre index and spatial coordinates
has been provided by the pipeline (Fig. 2.7 of the FLAMES manual). Note
this is a collapse of the whole spectrum. A narrow-band image in an emission-line
can look rather different. Also note that this image is not sky subtracted
(but the sky signal is available).